Marine organic-rich sediments are important for long-term carbon sequestration, and as a source of fossil hydrocarbons, but the processes underlying their formation remain elusive. We present a multiproxy analysis of a relatively recent, well-preserved Mediterranean organic-rich deposit known as sapropel S5, which formed 124–119 thousand years ago (ka B.P., where B.P. references year 1950). Combining planktonic foraminiferal abundance records with stable isotope and organic biomarker data, we reconcile the apparently contradicting coexistence of deep-dwelling foraminiferal faunas with green sulphur bacteria that indicate photic zone euxinia. S5 started with a rapid freshwater-induced increase of density stratification that inhibited vertical mixing and deepwater ventilation. Through the first 900 years, anoxic to euxinic deepwater conditions developed and extended up to roughly 200 m water depth. Then followed a 4100-year period of variability in the depth/intensity of winter mixing with a roughly 1400-year periodicity, coincident with fluctuations in water column stability. S5 terminated with a marked decrease in density stratification and consequently renewed convective overturn.